Thousands – perhaps tens of thousands – of California businesses are polluting streams, bays and the ocean, but state environmental regulators don’t know how many companies are doing how much damage.

In places like Logan Heights or National City, industry-filled neighborhoods send metals and toxic chemicals into the water, helping to ruin it for humans and poison it for marine life.

An entire regulatory system exists to prevent this – to keep businesses honest, residents safe and fish alive. That system is a mess.

At the beginning of last year, the city of San Diego estimated that 2,400 businesses here were operating without the necessary water pollution control permit. Many business owners may not know they’re violating the law; others are trying not to get caught.

At the end of the year, fewer than 400 businesses in San Diego had the permit.

By evading the law, businesses without a permit are propping up their bottom lines. The state estimates it costs $188,400 over five years for a business to get what’s known as an Industrial General Permit and comply with its requirements. The goal of the permit is to make sure companies are monitoring and reducing their water pollution.

Across the state, there could be thousands or even tens of thousands of businesses dodging these rules and sending unknown amounts of pollution into the state’s waters.

One problem is the state doesn’t know how many businesses it’s trying to regulate. There could be 20,000 companies in California that need to get a permit and reduce their water pollution. Or 100,000. Or 130,000.

Whatever the actual number – those are each estimates, no one knows for sure – only about 12,000 state businesses are complying with the regulations today.

“The vast majority of people, of facilities that should be doing something about water quality, are doing nothing,” said S. Wayne Rosenbaum, an attorney who represents businesses covered by the permit.

That’s a huge liability for them if they get caught: If 20,000 businesses should be following clean water rules, the statewide cost to comply might be about $3.7 billion over five years. If 100,000 businesses are covered by the rules, those costs could be nearly $19 billion.

Some current and former environmental regulators wonder if the rules that few are following even make sense.

In the early 1970s, the federal Clean Water Act created the ambitious goal of making every American waterway fishable and swimmable by the mid-1980s. That didn’t happen and is a long way off.

In San Diego, about 100 miles of bays, creeks, rivers and shoreline fail to meet federal water-quality standards.

At first, an interwoven network of federal, state and local regulations targeted the biggest polluters – the heavy industries and sewage treatment plants, which had been dumping pollution straight into the nation’s waters.

Since then, environmentalists have set their sights on smaller polluters and on urban “stormwater,” which is just water on the ground after it rains.

Stormwater sweeps up all kinds of debris and bits of pollution and then carries it out to the ocean. That pollution adds up: copper from brake pads, zinc from the coating on fences and roofs, oil from parking lots, grease from restaurants, pesticides from yards and trash from everywhere.

In 2015, the State Water Resources Control Board tried to get its arms around the problem by expanding its clean water rules to cover businesses that had been exempted from regulations but were still likely sources of pollution. Businesses from scrapyards to vineyards must now get an Industrial General Permit.

Yet, these sites still tend to be a low priority for many regulators, in part because there are so many of them.

“It’s a large permit, it’s a statewide permit and we’re outnumbered,” said Laurel Warddrip, the manager of the State Water Resources Control Board’s stormwater program.

There are about 75 stormwater regulators at State Water Board and nine regional boards that report to it, including the San Diego Regional Water Quality Control Board. They oversee not just industrial polluters but also pollution coming of the state’s highways, construction sites and sewer systems.

Over the past few years, though, the industrial sites have taken up a lot of their time.

The Industrial General Permit rules are supposed to be updated every five years. The new one was updated in 2014 and took effect in 2015. Before that, it hadn’t been updated since 1997.

When the state changed the rules to include more businesses, it arguably did something dumb: It made every business that already had a permit get a new permit. The businesses that had enrolled over the previous 17 years were suddenly kicked out of the system and forced to re-enroll.

David Gibson, executive director of the San Diego Regional Water Quality Control Board, said the state effectively doubled everybody’s workload. Now, regulators were not only trying to find new businesses that had to comply with the new rules but making sure the old ones got back in line.

Gibson is among those who believe all the attention on small industrial sites is sometimes misplaced. He favors figuring out the biggest threats to water quality and working to reduce those, rather than making sure everybody is doing their paperwork. But he doesn’t call the shots – the state does, and the state wanted everybody to get a new permit.

“It’s interesting, unfortunately, that we set out these goals of working on a watershed basis and identifying the pollutants of concern,” he said of his board’s own goals, “but it’s ultimately a bureaucratic decision that drives what you actually spend your time on.”

The state admits it doesn’t have the resources to make sure every business gets a permit. In fact, it doesn’t even think it can take a basic step that would ensure that most businesses at least know the permit exists: Send them a piece of mail saying so.

Warddrip said the state has thought about doing outreach to all the businesses that might need to get an Industrial General Permit, but is worried that effort will be more trouble than it’s worth.

“We dance around it, because to implement a statewide non-filer outreach effort is very expensive and is a huge staff workload,” she said.

If the state sent, say, 10,000 letters, it might have to answer 10,000 of replies or 10,000 phone calls. It would be totally swamped trying to enforce its own regulations.

It sometimes costs a lot to control a little pollution. Some pollution-control technologies are simple and inexpensive. A business can avoid stormwater rules if it’s operating indoors, out of the rain. A roof counts, a tarp might also work.

On the expensive end of the spectrum are high-end water treatment devices that use the same technologies desalination plants use to make ocean water drinkable.

Some businesses also try to capture all the water that comes on their property and then they pay truckers to carry it away. Others create small ponds for stormwater to run into, then they let it evaporate.

Some of the biggest companies – shipbuilders, like General Dynamics, for instance – are praised by environmentalists for doing the most to control their pollution, in part because of previous efforts by environmentalists to clean up those industries.

It’s now the smaller businesses that have environmentalists’ attention. In the past few years, several environmental groups have begun filing dozens of lawsuits against smaller industrial sites that are not complying with stormwater rules.

There’s plenty of places to go after.

In San Diego, a few thousand light industrial facilities are escaping oversight by the San Diego Regional Water Quality Control Board, according the city’s own pollution control team.

In January 2016, the city produced a list of about 2,400 businesses that it believes should get a pollution control permit but had not. They included bakeries, breweries, furniture-makers, printers, machine shops, limousine services, storage facilities and scrapyards.

At the end of the year, only about 260 businesses in the city had gotten a permit. About another 110 businesses in the city have gotten a “no exposure certification,” which means they are technically covered by the permit but don’t release any pollution. It costs $200 a year to get this certification, which is essentially the cost of telling the government one of its regulations doesn’t apply to you.

Even though the city identified businesses it thinks are breaking the law, the city’s job stops there. It doesn’t make them get a permit. Instead, it just sends its list to the regional board.

“The city is very diligent in our inspection process in making sure that we refer these businesses to the regional board to make sure they follow through on this state requirement,” said Drew Kleis, the deputy director of the city’s Division of Stormwater.

The board has found the city’s lists to be a waste of time.

Cynthia Gorham, an environmental engineer at the San Diego Regional Water Quality Control Board, said her team has visited businesses on the city’s lists and found they are “not conducting industrial activities that are actually subject” to the regulation.

In any case, neither the city nor the board will find much love as they go about doing their job, which is identifying small business owners that may suddenly be on the hook for mounds of paperwork and tens of thousands of dollars in new regulatory costs.

Ry Rivard is a reporter for Voice of San Diego. He writes about water and land use. You can reach him at ry.rivard@voiceofsandiego.org or 619.550.5665.